New version

.gitignore

@@ -2,4 +2,3 @@
 .Rhistory
 .RData
 .Ruserdata
-inst/doc

CaSpER.Rproj

@@ -18,4 +18,3 @@ StripTrailingWhitespace: Yes
 BuildType: Package
 PackageUseDevtools: Yes
 PackageInstallArgs: --no-multiarch --with-keep.source
-PackageRoxygenize: rd,collate,namespace,vignette

DESCRIPTION

@@ -8,7 +8,7 @@ Description: Identification, visualization and integrative analysis of CNV event
 Encoding: UTF-8
 LazyData: true
 LinkingTo: Rcpp
-Depends: Rcpp, signal, pheatmap, GenomicRanges, RColorBrewer, HMMcopy, IRanges, grid, ggplot2, reshape, mclust,  ggpubr, scales, gridExtra, igraph, intergraph, ggnetwork, ape, biomaRt, limma, GO.db, org.Hs.eg.db, GOstats
+Depends: Rcpp, signal, pheatmap, GenomicRanges, RColorBrewer, IRanges, grid, ggplot2, reshape, mclust,  ggpubr, scales, gridExtra, igraph, intergraph, ggnetwork, ape, biomaRt, limma, GO.db, org.Hs.eg.db, GOstats
 RoxygenNote: 6.1.1
 Suggests: knitr,
     rmarkdown

NAMESPACE

@@ -1,9 +1,11 @@
+useDynLib(CaSpER, .registration = TRUE)
 export(CreateCasperObject)
 export(lohCallMedianFilterByChr)
 export(lohCallMedianFilter)
 export(ProcessData)
 export(PerformMedianFilter)
 export(PerformMedianFilterByChr)
+export(PerformMeanFilterByChr)
 export(CenterSmooth)
 export(ControlNormalize)
 export(AverageReference)
@@ -19,6 +21,7 @@ export(extractEvents)
 export(draw_matrix2)
 export(draw_colnames_45)
 export(plotHeatmap)
+export(plotHeatmap10x)
 export(plotGEAndGT)
 export(plotLargeScaleEvent)
 export(plotBAFInSeperatePages)
@@ -41,13 +44,19 @@ export(splitByOverlap)
 export(extractLargeScaleEvents)
 export(mergeScalesAndGenerateFinalEventSummary)
 export(goEnrichmentBP)
+export(estimateTNoiseParamsMap)
+export(tdistPDF)
+export(dirichletpdf)
+export(normalize)
+export(manualSegment)
+export(processSegments)
+export(HMMsegment)
 export(gene.matrix)
 import(igraph)
 import(signal)
 import(pheatmap)
 import(RColorBrewer)
 import(grid)
-import(HMMcopy)
 import(IRanges)
 import(ggplot2)
 import(reshape)

R/casper.R

@@ -20,7 +20,7 @@
 #' 
 #' @slot loh  original baf signal 
 #' 
-#' @slot median.filtered.data  median filtered expression signal 
+#' @slot filtered.data  median filtered expression signal 
 #' 
 #' @slot loh.median.filtered.data  median filtered baf signal 
 #' 
@@ -30,9 +30,7 @@
 #' 
 #' @slot control.normalized  control normalization is performed by subtracting reference expression values from the tumor expression values. 
 #' 
-#' @slot control.normalized.visbound   control normalized data is thresholded in order to perform better visualization.
-#' 
-#' @slot control.normalized.visbound.noiseRemoved  noise is removed from control normalized and thresholded data.
+#' @slot control.normalized.noiseRemoved  noise is removed from control normalized and thresholded data.
 #' 
 #' @slot large.scale.cnv.events large scale CNV events identified by CaSpER
 #' 
@@ -78,12 +76,12 @@
 #' @aliases casper-class
 #' @exportClass casper
 
-casper <- methods::setClass("casper", slots = c(raw.data = "ANY", data = "ANY", median.filtered.data = "ANY", loh.median.filtered.data = "ANY", 
-    centered.data = "ANY", center.smoothed.data = "ANY", control.normalized = "ANY", control.normalized.visbound = "ANY", control.normalized.visbound.noiseRemoved = "ANY", 
+casper <- methods::setClass("casper", slots = c(raw.data = "ANY", data = "ANY", filtered.data = "ANY", loh.median.filtered.data = "ANY", 
+    centered.data = "ANY", matrix.type="ANY", center.smoothed.data = "ANY", control.normalized = "ANY", control.normalized.noiseRemoved = "ANY", 
     large.scale.cnv.events = "ANY", segments = "ANY", cytoband = "ANY", annotation = "ANY", annotation.filt = "ANY", control.sample.ids = "character", 
-    project.name = "character", genomeVersion = "ANY", hmmparam = "ANY", plotorder = "ANY", vis.bound = "ANY", 
-    noise.thr = "ANY", loh.name.mapping = "ANY", sequencing.type = "ANY", cnv.scale = "ANY", loh.scale = "ANY", method = "ANY", 
-    loh.shift.thr = "ANY", window.length = "ANY", length.iterations = "ANY", loh = "ANY"))
+    project.name = "character", genomeVersion = "ANY", hmmparam = "ANY", plotorder = "ANY",
+	 loh.name.mapping = "ANY", sequencing.type = "ANY", cnv.scale = "ANY", loh.scale = "ANY", method = "ANY", 
+    loh.shift.thr = "ANY", window.length = "ANY", length.iterations = "ANY", loh = "ANY", filter= "ANY"))
 
 setMethod(f = "show", signature = "casper", definition = function(object) {
     cat("An object of class", class(object), "in project", object@project.name, "\n", nrow(x = object@raw.data), "genes across", 

R/plots.R

@@ -62,6 +62,43 @@ draw_matrix2 <- function(matrix, border_color, gaps_rows, gaps_cols, fmat, fonts
 #' @export
 #'
 #'
+plotHeatmap10x <- function(object, fileName, cnv.scale = 3, cluster_cols = F, cluster_rows = T, show_rownames = T, only_soi = T) {
+
+    assignInNamespace(x = "draw_matrix", value = draw_matrix2, ns = asNamespace("pheatmap"))
+    assignInNamespace(x = "draw_colnames", value = "draw_colnames_45", ns = asNamespace("pheatmap"))
+
+
+    data <- object@control.normalized.noiseRemoved[[cnv.scale]]
+
+    x.center <- mean(data)
+    quantiles = quantile(data[data != x.center], c(0.01, 0.99))
+
+    delta = max( abs( c(x.center - quantiles[1],  quantiles[2] - x.center) ) )
+    low_threshold = x.center - delta
+    high_threshold = x.center + delta
+    x.range = c(low_threshold, high_threshold)
+
+    data[data < low_threshold] <- low_threshold
+    data[data > high_threshold] <- high_threshold
+
+    breaks <- seq(x.range[1], x.range[2], length=16)
+      #  breaks <- seq(0, 2, length=16)
+    color <- colorRampPalette(rev(brewer.pal(11, "RdYlBu")))(length(breaks))
+
+    idx <- cumsum(table(object@annotation.filt$Chr)[as.character(1:22)])
+    xlabel <- rep("", length(rownames(object@data)))
+    half <- round(table(object@annotation.filt$Chr)[as.character(1:22)]/2)[-1]
+    xpos <- c(half[1], (idx[-22] + half))
+    xlabel[xpos] <- 1:22
+
+    if (only_soi) 
+        data <- data[, !(colnames(data) %in% object@control.sample.ids)]
+
+    pheatmap(t(data), cluster_cols = F, cluster_rows = T, gaps_col = idx, color = color, breaks = breaks, 
+        labels_col = xlabel, show_rownames = T, filename = "heatmap.png")
+
+}
+
 plotHeatmap <- function(object, fileName, cnv.scale = 3, cluster_cols = F, cluster_rows = T, show_rownames = T, only_soi = T) {
 
     assignInNamespace(x = "draw_matrix", value = draw_matrix2, ns = asNamespace("pheatmap"))
@@ -76,13 +113,13 @@ plotHeatmap <- function(object, fileName, cnv.scale = 3, cluster_cols = F, clust
     xpos <- c(half[1], (idx[-22] + half))
     xlabel[xpos] <- 1:22
 
-    data <- object@control.normalized[[cnv.scale]]
+    data <- log2(object@control.normalized.noiseRemoved[[cnv.scale]])
 
     if (only_soi) 
         data <- data[, !(colnames(data) %in% object@control.sample.ids)]
 
     pheatmap(t(data), cluster_cols = F, cluster_rows = T, gaps_col = idx, color = color, breaks = breaks, 
-        labels_col = xlabel, show_rownames = T, filename = "test.png")
+        labels_col = xlabel, show_rownames = T, filename = "heatmap.png")
 
 }
 
@@ -622,9 +659,7 @@ plotSCellCNVTree <- function(finalChrMat, sampleName, path = "C:\\Users\\aharman
     colnames(m) <- rownames(finalChrMat)
     rownames(m) <- rownames(finalChrMat)
     tree <- Rfitch(na.omit(m), global = T, path = path, outgroup = T)
-
-
-
+
     pdf(fileName)
     X <- as.matrix(finalChrMat)[, which(apply(finalChrMat, 2, sum) != 0)]
     plot(tree, x.lim = 40, align.tip = TRUE, adj = 1, cex = 0.2)